Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    On the scaling of activity in tropical forest mammals
    Cid, Bruno ; Carbone, Chris ; Fernandez, Fernando A.S. ; Jansen, Patrick A. ; Rowcliffe, J.M. ; O'Brien, Timothy ; Akampurira, Emmanuel ; Bitariho, Robert ; Espinosa, Santiago ; Gajapersad, Krishna ; Santos, Thiago M.R. ; Gonçalves, André L.S. ; Kinnaird, Margaret F. ; Lima, Marcela G.M. ; Martin, Emanuel ; Mugerwa, Badru ; Rovero, Francesco ; Salvador, Julia ; Santos, Fernanda ; Spironello, Wilson R. ; Wijntuin, Soraya ; Oliveira-Santos, Luiz Gustavo R. - \ 2020
    Oikos 129 (2020)5. - ISSN 0030-1299 - p. 668 - 676.
    activity behavior - body mass - camera traps - diet - energy budget - predation risk

    Activity range – the amount of time spent active per day – is a fundamental aspect contributing to the optimization process by which animals achieve energetic balance. Based on their size and the nature of their diet, theoretical expectations are that larger carnivores need more time active to fulfil their energetic needs than do smaller ones and also more time active than similar-sized non-carnivores. Despite the relationship between daily activity, individual range and energy acquisition, large-scale relationships between activity range and body mass among wild mammals have never been properly addressed. This study aimed to understand the scaling of activity range with body mass, while controlling for phylogeny and diet. We built simple empirical predictions for the scaling of activity range with body mass for mammals of different trophic guilds and used a phylogenetically controlled mixed model to test these predictions using activity records of 249 mammal populations (128 species) in 19 tropical forests (in 15 countries) obtained using camera traps. Our scaling model predicted a steeper scaling of activity range in carnivores (0.21) with higher levels of activity (higher intercept), and near-zero scaling in herbivores (0.04). Empirical data showed that activity ranges scaled positively with body mass for carnivores (0.061), which also had higher intercept value, but not for herbivores, omnivores and insectivores, in general, corresponding with the predictions. Despite the many factors that shape animal activity at local scales, we found a general pattern showing that large carnivores need more time active in a day to meet their energetic demands.

    A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics
    Rovero, Francesco ; Ahumada, Jorge ; Jansen, Patrick A. ; Sheil, Douglas ; Alvarez, Patricia ; Boekee, Kelly ; Espinosa, Santiago ; Lima, Marcela Guimarães Moreira ; Martin, Emanuel H. ; O'Brien, Timothy G. ; Salvador, Julia ; Santos, Fernanda ; Rosa, Melissa ; Zvoleff, Alexander ; Sutherland, Chris ; Tenan, Simone - \ 2020
    Ecography 43 (2020)1. - ISSN 0906-7590 - p. 75 - 84.
    The understanding of global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110–200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g. habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.
    Types and characteristics of urban green & blue spaces having an impact on human mental health and wellbeing : Methods Protocol, Knowledge assessment and synthesis
    Andreucci, Maria Beatrice ; Vries, S. de; Marselle, Melissa R. ; Olszewska-Guizzo, Agnieszka ; Keune, Hans ; O'Brien, L. ; Russo, A. ; Remmen, Roy ; Davies, Zoe ; Livoreil, Barbara ; Beute, Femke ; Lammel, Annamaria - \ 2019
    EKLIPSE - 13 p.
    Working Group (EKLIPSE EWG) was formed to answer the following question: “Which types of urban and suburban blue and green spaces and which characteristics (components) of such spaces have a significant impact on human mental health and wellbeing?”. The answer will be provided by examining the scientific literature. Financial support from the World Health Organization (WHO), adding to that initially provided by EKLIPSE, will allow the EWG to conduct two separate systematic reviews (one for blue spaces and one for green spaces).
    Previous reviews have been focused on the local amount and availability of, or access to, green (and to a much lesser extent) blue space. The current systematic reviews will be unique in that they focus on the mental health benefits of the type of green (and blue) space and of its distinct characteristics (components).
    Each systematic reviews will follow six consecutive stages: 1) eligibility criteria for the articles will be formulated, 2) a systematic search strategy will be employed to yield relevant articles, 3) meta-data will be extracted and coded for each eligible study, 4) each study will be critically appraised, 5) a narrative and descriptive synthesis will be performed, and 6) outcomes of the synthesis will be discussed.
    The main deliverable of the project will be two reports (blue and green), but will also include dissemination via oral presentations and each systematic review will be published in a peer-reviewed journal. The outcomes of the systematic reviews will be aimed to inform and provide recommendations to (future) decision makers in several domains, such as health promotion, nature management, spatial policy, urban planning, and design.
    What Is Gender Equality in Science?
    O'Brien, Katherine R. ; Holmgren, Milena ; Fitzsimmons, Terrance ; Crane, Margaret E. ; Maxwell, Paul ; Head, Brian - \ 2019
    Trends in Ecology and Evolution 34 (2019)5. - ISSN 0169-5347 - p. 395 - 399.

    Why do inequalities persist between male and female scientists, when the causes are well-researched and widely condemned? In part, because equality has many dimensions. Presenting eight definitions of gender equality, we show each is important but incomplete. Rigid application of any single equality indicator can therefore have perverse outcomes.

    Camera trapping reveals trends in forest duiker populations in African National Parks
    O'Brien, Timothy G. ; Ahumada, Jorge ; Akampurila, Emmanuel ; Beaudrot, Lydia ; Boekee, Kelly ; Brncic, Terry ; Hickey, Jena ; Jansen, Patrick A. ; Kayijamahe, Charles ; Moore, Jennifer ; Mugerwa, Badru ; Mulindahabi, Felix ; Ndoundou-Hockemba, Mireille ; Niyigaba, Protais ; Nyiratuza, Madeleine ; Opepa, Cisquet K. ; Rovero, Francesco ; Uzabaho, Eustrate ; Strindberg, Samantha - \ 2019
    Remote Sensing in Ecology and Conservation (2019). - ISSN 2056-3485
    Abundance - Africa - bushmeat - camera trapping - Forest duikers - occupancy - protected areas - Royle-Nichols models

    Bushmeat hunting is widely cited as cause for declines of wildlife populations throughout Africa. Forest duikers (Bovidae, Cephalophinae) are among the most exploited species. Whether current harvest rates imperil duikers is debated because of the difficulty of accurately assessing population trends. To assess population trends, we first reviewed literature for historical duiker population estimates. Second, we used systematic camera-trap monitoring to assess population trends for 15 populations of nine duiker species in six national parks in Central and East Africa. We analysed annual monitoring data using Royle-Nichols heterogeneity-induced occupancy models to estimate abundance/sample point and derive occupancy estimates. Published density estimates indicate that duiker populations declined significantly throughout Africa between 1973 and 2013. There was a wide range of densities depending on species ((Formula presented.) range: 0.26–20.6 km−1) and whether populations were hunted ((Formula presented.) =6.3 km−1) or unhunted ((Formula presented.) = 16.3 km−1). More recent analysis of camera-trap monitoring produced different results. Estimated mean point abundance over time was between 0 and 0.99 individuals/point for four populations, between 1.0 and 1.99 for six populations, and greater than 2.0 for five populations. We observed five populations of duikers with negative trends in point abundances, although only one trend was significant and point abundance estimates for three populations were above 2.0 in the final survey year. Six populations showed positive trends in point abundance (three significant), and the remaining populations displayed no trends. Average occupancy was high (Ψ > 0.60) except for three populations. While literature indicates that historical population declines have occurred, most duiker populations appear relatively healthy in monitored parks. Our results indicate that these parks are effective in protecting most duikers despite hunting pressure. We recommend that systematic, standardized camera-trap monitoring be initiated in other African parks in combination with point-abundance models to objectively assess forest ungulate population trends.

    Data from: A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics
    Rovero, Francesco ; Ahumada, Jorge ; Jansen, Patrick ; Sheil, Douglas ; Alvarez, Patricia ; Boekee, Kelly ; Espinosa, Santiago ; Lima, Marcela Guimarães Moreira ; Martin, Emanuel H. ; O'Brien, Timothy G. ; Salvador, Julia ; Santos, Fernanda ; Rosa, Melissa ; Sutherland, Chris ; Tenan, Simone - \ 2019
    University of Florence
    community structure - conservation - functional traits - mammals - trophic guild - tropical forest - camera traps
    Understanding global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110-200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g., habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.Understanding global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110-200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g., habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.
    Developing sensor technologies to inform breeding approaches to reduce damaging behaviour in laying hens and pigs: The GroupHouseNet approach
    Rodenburg, T.B. ; Bennewitz, J. ; Haas, E.N. De; Košťál, L. ; Pichová, K. ; Piette, D. ; Tetens, J. ; Visser, B. ; Klerk, B. De; Sluis, M. Van Der; Zande, L.E. Van Der; Siegford, J. ; Toscano, M. ; Norton, T. ; Guzhva, O. ; Ellen, E.D. - \ 2019
    In: Precision Livestock Farming 2019. - Teagasc (Precision Livestock Farming 2019 - Papers Presented at the 9th European Conference on Precision Livestock Farming, ECPLF 2019 ) - ISBN 9781841706542 - p. 467 - 470.
    Automatic tracking - Damaging behaviour - Genetic selection

    The European COST Action GroupHouseNet aims to provide synergy for preventing damaging behaviour in group-housed pigs and laying hens. One area of focus of this network is how genetic and genomic tools can be used to breed animals that are less likely to develop damaging behaviour directed at their pen-mates. Reducing damaging behaviour in large groups is a challenge, because it is difficult to identify and monitor individual animals. With the current developments in sensor technologies and animal breeding, there is the possibility to identify individual animals, monitor individual behaviour, and link this information to the genotype. Using a combination of sensor technologies and genomics enables us to select against damaging behaviour in pigs and laying hens.

    Defining resilient pigs after a Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) challenge using activity and feeding data from accelerometers
    Zande, L.E. Van Der; Dunkelberger, J.R. ; Rodenburg, Bas ; Mathur, P.K. ; Cairns, W.J. ; Keyes, M.C. ; Eggert, J.M. ; Little, E.A. ; Dee, S.A. ; Knol, E.F. - \ 2019
    In: Precision Livestock Farming 2019. - Teagasc (Precision Livestock Farming 2019 - Papers Presented at the 9th European Conference on Precision Livestock Farming, ECPLF 2019 ) - ISBN 9781841706542 - p. 471 - 475.
    Accelerometers - Behaviour - Pig - PRRS - Resilience - RMSE

    Porcine reproductive and respiratory syndrome (PRRS) is an infectious viral disease in pigs. PRRS causes reproductive failure in sows and respiratory infections in growing pigs. To improve pig health and minimise economic losses, resilient pigs are preferred within the herd. Resilient pigs still become infected, yet are able to recover following infection, showing less variation in activity and feeding. In this study, 232 commercial crossbred pigs were equipped with individual accelerometer ear tags to monitor the number of active, feeding, and hyperactive events per individual per hour. At eight weeks of age, pigs were inoculated with PRRS virus 1-7-4. Data from accelerometers were collected 23 days prior to challenge and 42 days post-infection (dpi). Expected levels of activity, feeding, and hyperactivity were estimated by regressing behavioural traits on observed datapoints prior to challenge. This regression line was extended to 42 dpi. Then, deviations from the regression line were quantified as Root Mean Square Error (RMSE) for each individual during the following time periods: pre-challenge, 0-13 dpi, and 13-42 dpi. All traits decreased and RMSE increased post-challenge. These results are consistant with clinical signs of PRRS, including lethargy and loss of appetite. In addition, association of these traits with survival was also investigated. RMSE prior to PRRS-infection was not predictive of survival after infection. However, RMSE of feeding and activity during the peak challenge period (0-13 dpi) was predictive of survival, where pigs with less deviation in behaviour were more resilient to the PRRS challenge.

    TrackLab 2: A new solution for automatic recording of location, activity and social behaviour of group-housed animals
    Gijssel, A. Van; Loke, B.J. ; Ouweltjes, W. ; Rodenburg, T.B. ; Visser, E.K. ; Noldus, L.P.J.J. - \ 2019
    In: Precision Livestock Farming 2019. - Teagasc (Precision Livestock Farming 2019 - Papers Presented at the 9th European Conference on Precision Livestock Farming, ECPLF 2019 ) - ISBN 9781841706542 - p. 677 - 683.
    Health - Livestock - Monitoring - Multi-modal - TrackLab - Welfare

    The popularity of precision livestock farming is largely driven by a desire to optimise productivity, profitability and comfort. At the same time, there are growing societal concerns about animal welfare and animal health in relation to food safety and human health. These concerns can be addressed by academic and applied research into animal welfare and health indicators and increasingly by the utilisation of welfare and health metrics in operational farm management systems. TrackLab 2 is the latest tool for the measurement of livestock welfare and health indicators. It is designed to integrate and process multi-modal data for the capture of welfare and health indicators such as social behaviour, place-preference, activity, feeding and physiology. It was beta tested on four sites in the dairy cattle, poultry and pig farming domain. These first explorative tests revealed that TrackLab metrics are useful for both scientific, applied and commercial livestock research. TrackLab hardware is working well for large animals (cows, calves, pigs, sheep, poultry) but needs to be optimised for use on young birds and piglets. TrackLab 2 is also the first version to be applied in the operational farming context. The utilisation of welfare and health metrics in the operational context, to a level that exceeds the productivity focus, can prove a valuable asset in addressing societal concerns and enhancing livestock farming sustainability.

    Assessing individual activity levels in two broiler lines using an ultra-wideband tracking system
    Sluis, M. Van Der; Klerk, B. De; Ellen, E.D. ; Haas, Y. De; Hijink, T. ; Rodenburg, T.B. - \ 2019
    In: Precision Livestock Farming 2019. - Teagasc (Precision Livestock Farming 2019 - Papers Presented at the 9th European Conference on Precision Livestock Farming, ECPLF 2019 ) - ISBN 9781841706542 - p. 903 - 906.
    Activity - Broilers - Tracking - Ultra-wideband

    Individual data on activity of broilers is valuable for breeding programmes, as activity may serve as proxy for multiple health, welfare and performance indicators. However, in current husbandry systems, broilers are often kept in large groups, which makes it difficult to identify and monitor them at the individual level. Sensor technologies, such as ultra-wideband (UWB) tracking systems, might offer solutions. This paper investigated the recorded distances of an UWB tracking system that was applied to broilers, as a first step in assessing the potential of an UWB tracking system for studying individual levels of activity in broilers housed in groups. To this end, the distances moved as recorded by the UWB system were compared to distances recorded on video, using Kinovea video tracking software. There was a moderately strong positive correlation between the output of the UWB system and video tracking, although some under- and over- estimations were observed. Even though the recorded distances from the UWB system may not completely match the true distances moved, the UWB system appears to be well-suited for studying differences in activity between individual broilers when measured with the same system settings.

    Associating body condition score and parity with sub-optimal mobility in pasture-based dairy cows
    O'Connor, A.H. ; Bokkers, E.A.M. ; Boer, I.J.M. De; Hogeveen, H. ; Sayers, R. ; Byrne, N. ; Ruelle, E. ; Shalloo, L. - \ 2019
    In: Precision Livestock Farming 2019. - Teagasc (Precision Livestock Farming 2019 - Papers Presented at the 9th European Conference on Precision Livestock Farming, ECPLF 2019 ) - ISBN 9781841706542 - p. 798 - 802.
    Body condition - Claw disorder - Grass-based system - Lameness - Parity

    Sub-optimal mobility in dairy cows can be broadly defined as abnormal gait which causes a deviation from the optimal walking pattern of a cow. Sub-optimal mobility is also associated with significant economic and environmental consequences, which have yet to be extensively researched or quantified in pasture-based systems. However, to quantify sub-optimal mobility in terms of its impacts economically and environmentally, and indeed to aid in the development of automated detection sensors for sub-optimal mobility, a clear understanding of the characteristics of a cow with sub-optimal mobility is required. So far, automated detection sensors have been successful for detecting moderate to severe forms of sub-optimal mobility. However, there is a need for a better understanding of the cow-level traits associated with all forms of sub-optimal mobility, including mild forms, to incorporate this into future development of automated detection sensors for sub-optimal mobility. Therefore, the aim of our study was to determine the associations between hoof disorders (both type and presence), body condition score, and all levels of sub-optimal mobility in pasture-based dairy cows using data from a large sample of Irish dairy farms. Mobility scores, body condition scores (BCS), claw disorder (presence and severity), and parity records were available for 6,927 dairy cows from 52 pasture-based herds. Binomial logistic regression analysis was completed to determine the associations between claw disorder (presence and severity), BCS, parity and sub-optimal mobility. The output variable was sub-optimal mobility (mobility score ≥ 1) and the predictor variables were specific claw disorders and their severities, BCS, and parity. Our results indicate that all severities of claw disorders, low BCS, and higher parity cows are all associated with an increased risk for sub-optimal mobility.

    Field trial to demonstrate the intelligent dairy assistant (IDA) system on dairy farms
    Rutten, C.J. ; Molenaar, N. ; Hogewerf, P. ; Gosliga, S.P. Van; Lokhorst, C. - \ 2019
    In: Precision Livestock Farming 2019. - Teagasc (Precision Livestock Farming 2019 - Papers Presented at the 9th European Conference on Precision Livestock Farming, ECPLF 2019 ) - ISBN 9781841706542 - p. 277 - 283.
    Artificial intelligence - Health - Learning - Oestrus - Sensor

    Connecterra's Intelligent Dairy Assistant (IDA) is a novel Internet of Things based on a management support system for dairy farms. IDA uses sensor technology, cloud computing and artificial intelligence to support dairy farmers with insights on oestrus and health management. IDA analyses cow behaviour (originating from a 3D accelerometer on a neck collar) and herd patterns, and learns from the farmer's feedback. Within the Horizon 2020 project Internet for Food and Farm (www.IoF2020.eu) a field trial was conducted. The goal was to demonstrate that the IDA approach to generate actionable insights works. Therefore, we tracked KPI's on farm economics, animal health and fertility on two commercial dairy farms. We report the results of our trial from January to December 2018. Both farms had a herd of 100 cows, from which 50 cows were equipped with IDA. The farm KPI's were measured separately for the groups with and without. In comparison to the without group, the with group had, on average, its expected calving interval 5.92 and 0.88 days lower on Farm 1 and 2, respectively. Likewise, treatments with antibiotics 1.15 and 2.60 days shorter and 305 day milk yield 434 kg higher (Farm 1) and 405 kg lower (Farm 2) in the with group. For milk production the results are inconclusive as the groups were not balanced on milk yield before the trial started. We experienced in this trial, by qualitative feedback of the farmers, that the IDA approach worked and more observations are needed for scientific proof.

    Using a data lake in animal sciences
    Schokker, D. ; Athanasiadis, I.N. ; Visser, B. ; Veerkamp, R.F. ; Kamphuis, C. - \ 2019
    In: Precision Livestock Farming 2019. - Organising Committee of the 9th European Conference on Precision Livestock Farming (ECPLF), Teagasc, Animal and Grassland Research and Innovation Centre (Precision Livestock Farming 2019 - Papers Presented at the 9th European Conference on Precision Livestock Farming, ECPLF 2019 ) - ISBN 9781841706542 - p. 140 - 144.
    Animal experiment - Data lake - Scalability - Sensor data

    In the livestock domain, Big Data is becoming more common and is being anchored into the mind-set of researchers. With the increasing availability of large amounts of data of varying nature, there is the challenge of how to store, combine, and analyse these data efficiently. With this study, we explored the possibility of using a data lake for storing and analysing sensor data, using an animal experiment as the use case, to improve scalability and interoperability. The use case was an experiment within Breed4Food (a public-private partnership), in which the gait score of 200 turkeys was determined. In the experiment, a gait score was traditionally assigned to each animal by a highly-skilled person who visually inspected them walking. Next to it, a set of sensor data streams was recorded for each animal, specifically inertial measurement units (IMUs), a 3D-video camera, and a force plate, with the ambition to explore the effectiveness of these data streams as predictors for estimating the gait score. The resulting sensor output, i.e. raw data, were successfully stored in its original format in the data lake. Subsequently, for each sensor output we performed extract, transform, and load activities, by executing custom-made scripts to generate tab or comma separated files. Lastly, by using Apache Spark it was possible to easily perform parallel processing of the data, allowing for fast computing. In conclusion, we managed to set up a data lake, load animal experimental data and run preliminary analyses. The data lake allowed for easy scale up of both data loading and analyses, which is desired for dynamic analyses pipelines, especially when more data are collected in the future.

    Monitoring pig behaviour by RFID registrations
    Mol, R.M. De; Hogewerf, P.H. ; Verheijen, R.G.J.A. ; Dirx, N.C.P.M.M. ; Fels, J.B. Van Der - \ 2019
    In: Precision Livestock Farming 2019. - Teagasc (Precision Livestock Farming 2019 - Papers Presented at the 9th European Conference on Precision Livestock Farming, ECPLF 2019 ) - ISBN 9781841706542 - p. 315 - 321.
    Drinking behaviour - Eating behaviour - Pigs - RFID

    Automation of the monitoring of pig behaviour can support management; deviating behaviour can be an indicator for disease or other disturbances. Registrations of RFID at specific places in a pen can be used to estimate the individual pig behaviour in order to detect abnormalities in drinking and eating behaviour. LF RFID tags were applied to pigs in the period from weaning until the start of the fattening phase. This was done in several experiments at the Dutch Swine Innovation Centre in the South of the Netherlands. In each experiment, 12 pigs were monitored, each equipped with a RFID tag in the right ear. Three readers were installed at the drinking place: (1) and at the feeding trough (2) video recordings were available to validate the results from the processed RFID readings. The performance of the system depended on the established reading distance of the readers. Tag readings were combined into visits by applying a bout criterion. Visits were combined into meals by applying a meal criterion. A good correspondence between tag readings and observed visits was found. A longer reading distance resulted in more tag readings that did not coincide with eating or drinking (but with resting behaviour nearby). Combining the two readers at the feeding trough as if they were one gave better results. The derived visits and meals can be used for detection of deviations on the number per pig per day (or per pig per part of the day). This automated detection can be a valuable tool in pig farming.

    Machine learning to realize phosphate equilibrium at field level in dairy farming
    Mollenhorst, H. ; Haan, M.H.A. De; Oenema, J. ; Hoving-Bolink, A.H. ; Veerkamp, R.F. ; Kamphuis, C. - \ 2019
    In: Precision Livestock Farming 2019. - Teagasc (Precision Livestock Farming 2019 - Papers Presented at the 9th European Conference on Precision Livestock Farming, ECPLF 2019 ) - ISBN 9781841706542 - p. 41 - 44.
    Boosting - Crop yield - Machine learning - Manure - Phosphorus - Regression tree

    An important factor in circular agriculture is efficient application of animal manure. Therefore, input and output of nutrients, like phosphorus (P), need to be balanced. Currently, manure application is regulated with rather fixed P application norms as a generic translation of P yields of grassland and maize. Predicting P yields based on field specific, historical data could be an important step to better balance P input and output. This study's objective was to predict P yields based on field and weather data, using machine learning. The dataset contained 640 records of yearly crop yields per field between 1993-2016 with information on P input and output, irrigation, and soil status at field level as well as local weather data. Generalized boosted regression (GBR) was used to predict P yields for the last five years based on information from all previous years. Model performance was evaluated per year as well as together by plotting observed versus predicted values of all five years in one plot. This final plot was compared to a plot with the currently used generic application norms. Model performance per year showed that GBR could predict the trend from low to high rather well (correlations of ~0.8). Results of the five years together showed that GBR performance was better than the generic application norms (correlation 0.68 vs 0.59; RMSE 7.3 vs 8.2). In conclusion, GBR contributed to defining more flexible P application norms with the aim to realize a phosphate equilibrium.

    At-market sensor technologies to develop proxies for resilience and efficiency in dairy cows
    Ouweltjes, W. ; Haas, Y. De; Kamphuis, C. - \ 2019
    In: Precision Livestock Farming 2019. - Teagasc (Precision Livestock Farming 2019 - Papers Presented at the 9th European Conference on Precision Livestock Farming, ECPLF 2019 ) - ISBN 9781841706542 - p. 246 - 253.
    Feed efficiency - Precision livestock farming - Proxies - Resilience

    We hypothesise that at-market sensor technologies can be used to develop proxies for complex traits such as resilience and feed efficiency (FE). This was tested by comparing variables describing sensor data patterns (“curve-parameters”) from resilient or FE cows with non-resilient or non-FE cows. Sensor data included data from weighing scales, activity (steps) and rumination activity from neck collars, and milk production from the parlour or the milking robot. Curve-parameters were calculated for each sensor for each lactation for which data was available and included the mean, standard deviation (std), slope, skewness, and the autocorrelation. Data originated from a Wageningen Research farm, and included data from 1,800 cows with calvings between 1995-2016. During this time frame, there were 98 lactations with sufficient feed intake recordings to compute FE at lactation level (DMI (kg) / milk yield (kg)), and to rank them accordingly. The 1,800 cows that could be ranked according to their lifetime resilience (ability to re-calf in combination with the number of health and insemination events) based on scores for each of the, in total, 5,771 lactations. Subsequently, the 20% or 10% most and least FE or resilient lactations, respectively, were selected. Curve-parameters of these selected lactations were compared. Results imply that using a single sensor, or a single curve parameter, is likely to be insufficient as a proxy for resilience of efficiency. Future research should focus on studying which combination of curve parameters and sensors are most informative as proxy for these two complex traits.

    Local temperature and ecological similarity drive distributional dynamics of tropical mammals worldwide
    Beaudrot, Lydia ; Acevedo, Miguel A. ; Lessard, Jean Philippe ; Zvoleff, Alex ; Jansen, Patrick A. ; Sheil, Douglas ; Rovero, Francesco ; O’Brien, Timothy ; Larney, Eileen ; Fletcher, Christine ; Andelman, Sandy ; Ahumada, Jorge - \ 2019
    Global Ecology and Biogeography 28 (2019)7. - ISSN 1466-822X - p. 976 - 991.
    coexistence - dynamic occupancy modelling - imperfect detection - occupancy–environment association - range shift - species distribution - species interactions

    Aim: Identifying the underlying drivers of species’ distributional dynamics is critical for predicting change and managing biological diversity. While anthropogenic factors such as climate change can affect species distributions through time, other naturally occurring ecological processes can also have an influence. Theory predicts that interactions between species can influence distributional dynamics, yet empirical evidence remains sparse. A powerful approach is to monitor and model local colonization and extinction—the processes that generate change in distributions over time—and to identify their abiotic and biotic associations. Intensive camera-trap monitoring provides an opportunity to assess the role of temperature and species interactions in the colonization and extinction dynamics of tropical mammals, many of which are species of conservation concern. Using data from a pan-tropical monitoring network, we examined how short-term local temperature change and ecological similarity between species (a proxy for the strength of species interactions) influenced the processes that drive distributional shifts. Location: Tropical forests worldwide. Time period: 2007–2016. Major taxa studied: Terrestrial mammals. Methods: We used dynamic occupancy models to assess the influence of the abiotic and biotic environment on the distributional dynamics of 42 mammal populations from 36 species on 7 tropical elevation gradients around the world. Results: Overall, temperature, ecological similarity, or both, were linked to colonization or extinction dynamics in 29 populations. For six species, the effect of temperature depended upon the local mammal community similarity. This result suggests that the way in which temperature influences local colonization and extinction dynamics depends on local mammal community composition. Main conclusions: These results indicate that varying temperatures influence tropical mammal distributions in surprising ways and suggest that interactions between species mediate distributional dynamics.

    Towards a general framework for the assessment of interactive effects of multiple stressors on aquatic ecosystems : Results from the Making Aquatic Ecosystems Great Again (MAEGA) workshop
    Brink, Paul J. Van den; Bracewell, Sally A. ; Bush, Alex ; Chariton, Anthony ; Choung, Catherine B. ; Compson, Zacchaeus G. ; Dafforn, Katherine A. ; Korbel, Kathryn ; Lapen, David R. ; Mayer-Pinto, Mariana ; Monk, Wendy A. ; O'Brien, Allyson L. ; Rideout, Natalie K. ; Schäfer, Ralf B. ; Sumon, Kizar A. ; Verdonschot, Ralf C.M. ; Baird, Donald J. - \ 2019
    Science of the Total Environment 684 (2019). - ISSN 0048-9697 - p. 722 - 726.
    Aquatic ecosystems - Ecological models - Ecological risk assessment framework - Multiple stressors - Workshop

    A workshop was held in Wageningen, The Netherlands, in September 2017 to collate data and literature on three aquatic ecosystem types (agricultural drainage ditches, urban floodplains, and urban estuaries), and develop a general framework for the assessment of multiple stressors on the structure and functioning of these systems. An assessment framework considering multiple stressors is crucial for our understanding of ecosystem responses within a multiply stressed environment, and to inform appropriate environmental management strategies. The framework consists of two components: (i) problem identification and (ii) impact assessment. Both assessments together proceed through the following steps: 1) ecosystem selection; 2) identification of stressors and quantification of their intensity; 3) identification of receptors or sensitive groups for each stressor; 4) identification of stressor-response relationships and their potential interactions; 5) construction of an ecological model that includes relevant functional groups and endpoints; 6) prediction of impacts of multiple stressors, 7) confirmation of these predictions with experimental and monitoring data, and 8) potential adjustment of the ecological model. Steps 7 and 8 allow the assessment to be adaptive and can be repeated until a satisfactory match between model predictions and experimental and monitoring data has been obtained. This paper is the preface of the MAEGA (Making Aquatic Ecosystems Great Again) special section that includes three associated papers which are also published in this volume, which present applications of the framework for each of the three aquatic systems.

    Detecting tropical wildlife declines through camera-trap monitoring : An evaluation of the Tropical Ecology Assessment and Monitoring protocol
    Beaudrot, Lydia ; Ahumada, Jorge ; O'Brien, Timothy G. ; Jansen, Patrick A. - \ 2019
    Oryx 53 (2019)1. - ISSN 0030-6053 - p. 126 - 129.
    Camera trap - conservation - monitoring - power analysis - sampling design - Tropical Ecology Assessment and Monitoring - wildlife management

    Identifying optimal sampling designs for detecting population-level declines is critical for optimizing expenditures by research and monitoring programmes. The Tropical Ecology Assessment and Monitoring (TEAM) network is the most extensive tropical camera-trap monitoring programme, but the effectiveness of its sampling protocol has not been rigorously assessed. Here, we assess the power and sensitivity of the programme's camera-trap monitoring protocol for detecting occupancy changes in unmarked populations using the freely available application PowerSensor!. We found that the protocol is well suited to detect moderate (≥ 5%) population changes within 3-4 years for relatively common species that have medium to high detection probabilities (i.e. p > 0.2). The TEAM protocol cannot, however, detect typical changes in rare and evasive species, a category into which many tropical species and many species of conservation concern fall. Additional research is needed to build occupancy models for detecting change in rare and elusive species when individuals are unmarked.

    A Bifidobacterial pilus-associated protein promotes colonic epithelial proliferation
    O'Connell Motherway, Mary ; Houston, Aileen ; O'Callaghan, Grace ; Reunanen, Justus ; O'Brien, Frances ; O'Driscoll, Tara ; Casey, Patrick G. ; Vos, Willem M. de; Sinderen, Douwe van; Shanahan, Fergus - \ 2019
    Molecular Microbiology 111 (2019)1. - ISSN 0950-382X - p. 287 - 301.

    Development of the human gut microbiota commences at birth, with certain bifidobacterial species representing dominant and early colonisers of the newborn gastrointestinal tract. The molecular basis of Bifidobacterium colonisation, persistence and presumed communication with the host has remained obscure. We previously identified tight adherence (Tad) pili from Bifidobacterium breve UCC2003 as an essential colonisation factor. Here, we demonstrate that bifidobacterial Tad pili also promote in vivo colonic epithelial proliferation. A significant increase in cell proliferation was detectable 5 days postadministration of B. breve UCC2003. Using advanced functional genomic approaches, bacterial strains either (a) producing the Tad2003 pili or (b) lacking the TadE or TadF pseudopilins were created. Analysis of the ability of these mutant strains to promote epithelial cell proliferation in vivo demonstrated that the pilin subunit, TadE, is the bifidobacterial molecule responsible for this proliferation response. These findings were confirmed in vitro using purified TadE protein. Our data imply that bifidobacterial Tad pili may contribute to the maturation of the naïve gut in early life through the production of a specific scaffold of extracellular protein structures, which stimulate growth of the neonatal mucosa.

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